AMMAN, Jordan — President Trump threatened to retaliate against aid recipients like Jordan for having denounced his decision in December to recognize Jerusalem as Israel’s capital. But on Wednesday, his top diplomat gave Jordan more money.

In a remarkably cordial reception that contrasted sharply with Vice President Mike Pence’s visit last month, Secretary of State Rex W. Tillerson signed an agreement that guarantees Jordan nearly $1.3 billion in annual assistance from the United States for the next five years.

The aid pact, an increase over the roughly $1 billion in current annual aid to Jordan, was all the more striking because the Trump administration has proposed eliminating much of America’s foreign assistance budget.

The increase partly reflected Jordan’s longtime role as an important partner in fighting extremism in the region and housing millions of refugees from the Syria war.

But it also appeared to show the value the administration places on Jordan regarding the Israeli-Palestinian conflict, even though Jordan was among the 128 members of the United Nations that voted to condemn the United States two months ago over Mr. Trump’s decision on Jerusalem, the contested holy city that Palestinians want part of as their future capital.

When Mr. Pence visited Jordan in January, King Abdullah II gave him an unusually stern and public lecture about the Jerusalem decision.

“For us, Jerusalem is key to Muslims and Christians as it is to Jews,” Abdullah said. “It is key to peace in the region.”

With Mr. Tillerson, Jordanian officials were far less hectoring, as Abdullah kept his meeting with Mr. Tillerson private. Foreign Minister Ayman Safadi of Jordan, who signed the aid agreement with Mr. Tillerson at a ceremony, referred to the Jerusalem decision only when asked, and briefly at that.

“As you know, we made our position on Jerusalem clear and we view these final-status issues as needing to be negotiated among the parties on the basis of a final solution,” Mr. Safadi said while sitting beside Mr. Tillerson. “The challenge is how to move forward and make sure it does not get worse.”

The softer response may have partly resulted from the passage of several weeks’ time, or the signing of the aid agreement. Or maybe it was because Mr. Pence had stood smiling behind President Trump when he made the announcement about Jerusalem, while Mr. Tillerson was nowhere to be seen. Or maybe it was because Mr. Tillerson was known to have successfully lobbied President Trump to only halve funding for the United Nations agency that provides aid to millions of Palestinian refugees instead of eliminating it altogether, as Ms. Haley and others in the White House were known to have advocated.

The relief agency underwrites schools and health clinics that serve hundreds of thousands of Palestinian refugees in Jordan.

Mr. Tillerson also made clear during his Jordan visit that he was not directly involved in the Trump administration’s long-awaited Middle East peace plan between Israelis and Palestinians. While describing it as “fairly well advanced,” Mr. Tillerson said it was up to Mr. Trump to decide when to release the plan.

Jared Kushner, the president’s son-in-law and senior adviser, and Jason D. Greenblatt, Mr. Trump’s special Middle East envoy, have been developing the plan, which has largely excluded Mr. Tillerson and the State Department. Palestinian leaders have in recent months refused to participate in talks about the plan to protest Mr. Trump’s Jerusalem decision.

“I have seen the elements of the plan that’s been under development for a number of months,” Mr. Tillerson said at a news conference in Jordan’s Ministry of Foreign Affairs and Expatriates. “I have consulted with them on the plan and identified areas that we feel need further work.”

But he said the plan and the timing for its release were in Mr. Trump’s hands.

“I think it’ll be up to the president to decide when he feels it’s time and he’s ready to put that plan forward,” Mr. Tillerson said.

Israel is conspicuously not on the itinerary for Mr. Tillerson, who has been in the Middle East all week, including on Monday when the Trump administration announced its budget for fiscal year 2019, which proposed slashing the department’s spending on global health initiatives by 30 percent.

Millions of Africans depend on AIDS drug regimens purchased with those funds, and health advocates have estimated that the Trump administration’s proposed cuts would cost hundreds of thousands of lives.

Mr. Tillerson said that the administration is hoping that other countries and aid organizations step in with funding as the United States retreats. One of the few countries that has been increasing its assistance around the world is China, but Mr. Tillerson spent much of last week in South America, where he warned countries against taking Chinese aid.

A version of this article appears in print on , on Page A12 of the New York edition with the headline: Jordan Gets More Aid From U.S. Despite Rancor Over Jerusalem. Order Reprints | Today’s Paper | Subscribe